title: Comparative transcriptome analysis in monocyte-derived macrophages of asymptomatic GBA mutation carriers and patients with GBA-associated Parkinson’s disease

status: Public on Sep 29 2021

city: Gatchina

first: Katerina

last: Basharova

address: 1, mkr. Orlova roshcha

institute: NRC "Kurchatov Institute" - PNPI

summary: We compared transcriptome of monocyte-derived macrophages of 5 patients with GBA-PD (4 L444P/N, 1 N370S/N) and 4 asymptomatic GBA mutation carriers (GBA-carriers) (3 L444P/N, 1 N370S/N) and 4 controls. We also conducted comparative transcriptome analysis for L444P/N only GBA-PD patients and GBA-carriers. Revealed deregulated genes in GBA-PD independently of GBA mutations (L444P or N370S) were involved in immune response, neuronal function. We found upregulated pathway associated with zinc metabolism in L444P/N GBA-PD patients. The potential important role of DUSP1 in the pathogenesis of GBA-PD was suggested.

overall_design: 5 patients with GBA-PD and 4 GBA-carriers and also 4 neurological healthy individuals were enrolled for the current study

first: Tatiana

last: Usenko

first: Anastasia

last: Bezrukova

first: Alexandra

last: Panteleeva

first: Mikhail

last: Nikolaev

first: Alena

last: Kopytova

first: Irina

last: Miliukhina

first: Anton

last: Emelyanov

first: Ekaterina

last: Zakharova

first: Sofya

last: Pchelina


title: Application of a Agilent hydatid  4x44k - cDNA microarray for identification of dihydroartemisinin targeting genes in Echinococcus granulosus larval protoscoleces

city: Urumqi

first: Limei

last: Wen

address: No. 137 Liyushan South Road, Pharmaceutical Department

country: China

institute: The First Affiliated Hospital of Xinjiang Medical University

summary: A cDNA microarray composed of 9306 uniEST probes was constructed andapplied to detect the gene expression profile of protoscoleces of E. granulosus treated with dihydroartemisinin in vitro, respectively. Compared with the untreated protoscoleces, 752 genes were up-regulated and 269 genes were down-regulated in protoscoleces treated with dihydroartemisinin. The differential expression genes in protoscoleces induced by dihydroartemisinin were clustered into molecular metabolic process, cell development and differentiation, anatomical structure morphogenesis and formation, and were enriched in calcium signaling pathway, protein processing in endoplasmic reticulum (ER), molecular metabolism and synthesis, Wnt signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway.

overall_design: Isolated E. granulosus protoscoleces were treated with dihydroartemisinin and was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China).

first: Jianhua

last: Wang


title: Single cell RNA-seq analysis of Mitochondrial ROS low CD34+ cells and Mitochondrial ROS high CD34+ cells

status: Public on Sep 30 2021

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

country: USA

institute: Indiana University

type: Expression profiling by high throughput sequencing

summary: Ex vivo cultured human cord blood CD34+ cells were sorted as Mitochondrial ROS low cells(15%) and Mitochondiral ROS high cells (15%). These two populations were analyzed by single cell RNA-seq. Totally 18 cell clusters were identified by UMAP analysis.One of the clusters enriched with AVP, HLF,CD34, PROM1, MLLT3 and MSI2 was proved by in vivo transplantation experiments as the functional hematopoietic stem cell population.  ADGRG1 combined with CD34 and PROM1 could be used to enrich functional hematopoietic stem cell upon ex vivo culture stress.

overall_design: Fresh humn cord blood CD34+ cells were ex vivo cultured in Stemline II medium with growth factors. At day 4, cells were sorted by FACS as Mitochondiral ROS low and Mitochondrial ROS high CD34+ cell populations. 10X single cell RNA-seq analysis was performed to analyze these two CD34+ cell populations with different mitochondrial ROS levels.

first: Yandan

last: Chen

first: Shuyi

last: Fang

first: Jun

last: Wan


title: hBD2 in Murine Cigarette Smoke Exposure

city: Hamilton

first: Nadia

last: Milad

state: Ontario

address: 1280 Main St W

country: Canada

institute: McMaster University

summary: Cigarette smoke exposure induces pulmonary inflammation despite increased risk of lung infection. We tested the ability of human beta-defensin 2, an antimicrobial peptide, to modulate inflammatory processes while promoting immune competence.

overall_design: n=4-5 per group, 4 groups, RA-Veh = room air-exposed vehicle-treated, RA-hBD2 = room air-exposed hBD2-treated, CS-PBS = cigarette smoke-exposed vehicle-treated, and CS-hBD2 = cigarette smoke-exposed hBD2-treated


title: HumanCervical Cancer Cell Line: Control vs. HOXD9 knock out

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: NOT PROVIDED; REQUESTED

overall_design: HOXD9 gene was repressed in SKG1 cervical cancer cells and gene expression was compared with that in control cells.

first: Takashi

last: Iwata


title: p53 ablation fails to completely rescue microcephaly caused by impaired minor intron splicing

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Mutations in the minor spliceosome components such as RNU4atac, a small nuclear RNA (snRNA), are linked to primary microcephaly. We have reported that in the conditional knockout (cKO) mice for Rnu11, a minor spliceosome snRNA, minor intron splicing defect in minor intron-containing genes (MIGs) regulating cell cycle resulted in cell cycle defect with a concomitant increase in yH2aX+ cells and P53-mediated apoptosis. Trp53 ablation in the Rnu11 cKO mice did not prevent microcephaly. Although RNAseq analysis of the double knockout (dKO) pallium reflected transcriptomic shift towards the control from the cKO. We found elevated minor intron retention and alternative splicing across minor introns in the dKO. Disruption of these minor intron-containing genes (MIGs) resulted in cell cycle defect that was detected earlier and was more severe in the dKO, but with delayed detection of yH2aX+ DNA damage. Thus, P53 might also play a role in causing DNA damage in the developing pallium. In all, our findings further refine our understanding of the role of the minor spliceosome in cortical development and identify MIGs underpinning microcephaly in minor spliceosome-related disease.

overall_design: Total mRNA profiles of pallia from E13.5 (n=4) control, Rnu11 cKO, and Rnu11::Trp53 dKO embryos through TruSeq stranded total RNA prep followed by Illumina NextSeq500 with high output.

first: Alisa

middle: K

last: White


title: Small RNA sequencing of the 8 to 30-nucleotide window from various samples

city: Montréal

first: Tarik

last: Moroy

address: 110 Pine Ave W, Montreal

institute: IRCM

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have challenged this dogma by preserving ribosomal RNA (rRNA) in our samples and by lowering the minimal RNA size window of our small RNA-Seq analyses to 8 nt

sample_organism:
Arabidopsis thaliana
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Analyzing the content of the RNA size window between 8 and 30 nt of 13 different biological samples from 6 different organisms by small RNA-Seq.

first: Patrick

last: Provost

first: Charles

middle: J

last: Beauparlant

first: Marine

last: Lambert

first: Abderrahim

last: Benmoussa


title: Lignin production associated genes in Urochloa humidicola

city: Juiz de Fora

first: Ana Luisa

middle: Sousa

last: Azevedo

state: Minas Gerais

address: Rua Eugenio do Nascimento, 610

country: Brazil

institute: Empresa Brasileira de Pesquisa Agropecuaria

summary: This study aims to reveal genes related to lignin production in Urochloa humidicola through RNA-Seq. This species is widely used as forrage for cattle, being some species of Urochloa responsible for 85% of pastures in Brazil. Given this importance, lignin is a molecule directly related to low digestibility in cattle. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The second extended leaves were collected for RNA extraction using RNeasy® Plant Mini Kit. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. As Urochloa humidicola does not have a sequenced genome, a transcriptome assembly was built by two approaches: through Trinity v 2.8.4 (Grabherr et al., 2011), and Stringtie v 2.0.4 software (Pertea et al., 2015), using Urochloa ruziziensis as reference genome. Then, the final transcriptome was assembled using those two de novo assembles by PASA v 2.2 (Haas et al., 2003). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 123 million reads were sequenced. The final assembled transcriptome was formed by 48,695 transcripts. The differential expressed genes analysis revealed 258 significatively genes. Here, we highlighted genes related to flavonoid biosynthetic process, regulation of phenylpropanoid metabolic process, and Myb-like DNA-binding domain.

overall_design: We selected four low lignin production samples, and four high lignin production samples, according to previous study that avaliate lignin percentage.

first: Machado

last: Marco Antonio


title: MicroRNA-sequencing from the striatum of ELAVL4 (HuD) KO mice and wild type littermate adult mice

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

summary:
Purpose: The goals of this study are to determine how deletion of the RNA-binding protein HuD affects the levels of microRNAs in the striatum of Elav4 (HuD) KO using miRNA-seq
Methods: Total RNA from striatum of male adult  Elavl4 (HuD) KO and wild-type (WT) littermates (n=3 per genotype) crossbred to  C57Bl/6 for more than 10 generations were analyzed by small RNA sequencing, in triplicate, using an Illumina NextSeq platorm. The percentage of the number of bases with Q >30 for all 6 samples were >93%.
Results: Using an optimized data analysis workflow (see diagram below), about 6.3 million sequence reads per HuD KO sample and 3.3 million per WT sample were mapped  miRBase v22. The expression level (Reads count) of miRNAs were calculated using miRDeep2. The number of identified miRNA per group was calculated based on the mean of CPM in group > 1.
Conclusions: We found 309 miRNAs from 54 unique families (FC>1.75- and p<0.05) were significantly upregulated while 161 miRNAs from 143 unique families (FC<0.55 and p<0.05) were significantly downregulated in the striatum of HuD KO mice  vs WT samples.

overall_design: Striatal miRNA profiles of adult male wild type (WT) and Elavl4 -/- (HuD KO) mice


title: In Vitro Reconstitution of the Whole Male Germ-Cell Development from Mouse Pluripotent Stem Cells [RNA-Seq]

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: Mammalian male germ-cell development consists of three distinct phases: primordial germ cell (PGC) development, male germ-cell specification for spermatogonium development, and ensuing spermatogenesis. Here, we show an in vitro reconstitution of whole male germ-cell development by pluripotent stem cells (PSCs). Mouse embryonic stem cells (mESCs) are induced into PGC-like cells (mPGCLCs), which are expanded for epigenetic reprogramming. In reconstituted testes under an optimized condition, such mPGCLCs differentiate into spermatogonium-like cells with proper developmental transitions, gene expression, and cell-cycle dynamics and are expanded robustly as germline stem cell-like cells (GSCLCs) with an appropriate androgenetic epigenome. Importantly, GSCLCs show vigorous spermatogenesis, not only upon transplantation into testes in vivo but also under an in vitro culture of testis transplants, and the resultant spermatids contribute to fertile offspring. By uniting faithful recapitulations of the three phases of male germ-cell development, our study creates a paradigm for the in vitro male gametogenesis by PSCs.

overall_design: Transcriptome analysis of mouse spermatogonia and germline stem cell-like cells.

first: Yukiko

last: Ishikura

first: Hiroshi

last: Ohta

first: Takuya

last: Sato

first: Yusuke

last: Murase

first: Yoji

last: Kojima

first: Chika

last: Yamashiro

first: Tomonori

last: Nakamura

last: Yamamoto

first: Takehiko

last: Ogawa

first: Mitinori

last: Saitou


title: Cxcr3+ CD62L+ effector CD8+ T cells function as  precursor of central memory cells

city: Chongqing

first: Haiyang

last: He

address: Gaotanyan street

institute: Arm medical university

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Effector and memory P14 CD8+ T cells were sorted by flow cytometry at 8 days (d8) and 30 days (d30) after LCMV Armstrong virus infection respectively for scRNAseq analysis

first: Xinyuan

last: Zhou


title: Effect of NF-kappa B (NF-kB) p50 (Nfkb1) deletion on ozone-induced pulmonary transcriptome changes in mice

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Background: Ozone (O3) is the predominant oxidant air pollutant associated with respiratory inflammation, lung dysfunction, and worsening preexisting airway diseases. We previously determined that lack of NF-kB signlaing pathway suppressed lung injury and inflammation caused by O3 in mice. The current study was to determine transcriptome mechanisms orchestrated by NF-kB during the development of pulmonary O3 injury.
Methods: To investigate the role of NF-kB1 pathway in  lung gene expression changes, Nfkb1-deficient (Nfkb1-/-) and wild-type (Nfkb1+/+) mice were exposed to air or 0.3-ppm O3. Total RNAs were isolated from lung homogenates and cDNA microarray analyses were performed to elucidate NF-kB1-directed transcriptomics in basal lungs (air-exposed) as well as in the lung exposed to O3 (48 hr).
Results: In air-exposed Nfkb1-/- lungs, leukocyte extravasation/adhesion and antigen presentation genes were overexpressed while immunity genes were suppressed, supporting the dual role of Nf-kB1 homodimer as a transcriptional repressor as well as transcriptional activator and the phenotype of Nfkb1-/- mice (defective response to infection and specific antibody production). After O3 exposure. Nfkb1-/- mice showed suppressed expression of lung cell cycle genes and enhanced expression of DNA damage checkpoint regulation pathway genes, compared to Nfkb1+/+ mice.
Conclusion: Overall, deficiency of NF-kB1 in mouse lungs altered transcriptomes to protect lungs from O3-induced inflammation, cell proliferation, and DNA damages.

overall_design: PARALLEL study design with 12 samples comparing 4 groups  of gene and exposure: (2 groups Nfkb1+/+ wild type; air-48 hr O3 exposure)  (2 groups Nfkb1-/- knockout; air-48 hr O3 exposure). Biological replicates: 3 per group.

first: Steven

last: Kleeberger

first: Hye-Youn

last: Cho


title: The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during normal and pathogenic angiogenesis

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of tumor necrosis factor receptor (Tnfr) deletion in ozone-induced pulmonary transcriptome changes in mice

summary:
Background: Ozone (O3) is the predominant oxidant air pollutant associated with respiratory inflammation, lung dysfunction, and worsening preexisting airway diseases. We determined that TNFR signlaing pathway plays a key role in lung injury and inflammation caused by O3 in mice. However, downstream molecular mechanisms underlying TNFR pathway have not been investigated.
Methods: To investigate the role of TNFR pathway in  gene expression changes, Tnfr1/2-deficient (Tnfr-/-) and wild-type (Tnfr+/+, C57BL/6J) mice were exposed to air or 0.3-ppm O3. Total RNAs were isolated from lung homogenates and cDNA microarray analyses were performed to elucidate TNFR-directed transcriptomics in basal lungs (air-exposed) as well as in the lung exposed to time course of O3 (24, 48, and 72 hr).
Results: O3 caused time-dependent changes in lung gene expressions with the greatest transcriptome changes at 48-72 hr of exposure in Tnfr+/+ mice. At early time of exposure (24 hr), acute phase and inflammatory responses gene as well as redox and lipid metabolism genes were increased by O3 while cell cycle and DNA damage repair genes were markedly increased by O3 at later time points (48-72 hr). Compared to Tnfr+/+ mice, Tnfr-/- mice had lowered expression of inflammatory response and vascular disorder-related genes at baseline (air).  After O3 exposure, Tnfr-/- had enhanced expression of immune and inflammatory genes at 24 hr, indicating compensatory or adpative poentiation of immunity in Tnfr-/- mice. At 48 hr of O3 exposure, Tnfr-/- mice showed suppressed expression of genes involved in epithelial proliferation, inflammatory cell influxes and epithelial injury, compared to Tnfr+/+ mice. At 72 hr of O3 exposure,  neurodegeneration and neurotransmitter transport genes were suppressed in Tnfr-/- than in Tnfr+/+.
Conclusion: Overall, deficiency of TNFR-mediated signaling in mouse lungs altered transcriptomes to protect lungs from O3-induced inflammation, cell proliferation, oxidative stress, and neuronal disorders.

overall_design: PARALLEL study design with 24 samples comparing 8 groups  of gene and exposure: (4 groups Tnfr+/+ wild type; air-24 hr O3-48 hr O3-72 hr O3 exposure)  (4 groups Tnfr knockout; air-24 hr O3-48 hr O3-72 hr O3 exposure). Biological replicates: 3 per group.


title: Sex differences in gene expression of developing fetal brain in pig

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

summary: In this study, gene expression was profiled by RNA-seq to examine whole transcriptome of the male and female fetal brain of domesticated pig on the three gestation days 45, 60 and 90. Gene expression in fetal brain was distinct on day 90 compared to days 45 and 60. The homeobox genes were consistently upregulated in the brain of females compared to males during development. The sex of adjacent fetuses influenced gene expression of fetal brain. Extensive exon-level expression changes in the developing brains was observed. Pathway enrichment analysis showed that the ionotropic glutamate receptor pathway and p53 pathway were enriched in female brain only whereas receptor mediated signaling pathways were enriched in the male brain alone. Genes that are known markers of neurons and astrocytes were differentially regulated in male and female brain during development. The study further suggests that regulation of ion transportation via placental matrotrophy may play a role in fetal brain development.

overall_design: Total 18 fetal brain samples (3 gestation days x 2 sexes x 3 biological replicates) were used for RNA sequencing.  The three gestation times are days 45, 60 and 90. Total RNA of each sample was used to prepared Illumina sequencing libraries were prepared from the was performed by the Novogen Cooperation Inc. (8801 Folsom Blvd #290, Sacramento, CA 95826). Each library was sequenced to depth of 20 million paired end reads of 150 bases using NovaSeq 6000.

first: Monica

last: Strawn

first: Joao

middle: G

last: Moraes

first: Timothy

last: Safranski


title: Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens

city: Mueang Nakhon Ratchasima

first: Panpradub

last: Sinpru

state: Nakhon Ratchasima

address: Maha Witthayalai Rd

department: School of Animal Technology and Innovation

country: Thailand

institute: Suranaree University of Technology

summary: Slow-growing Korat chicken (KR) is an alternative to broiler chickens that has been used as a national tool to support smallholder farmers due to a higher selling price of KR meat. However, the individual variability of feed efficiency (FE) within a KR stockbreeding results in a lack of competitiveness. Therefore, improvement of FE of KR is of major importance to improve the profitability of livestock production enterprises. Here, we selected two groups of KR with divergent feed conversion ratios (FCR). We performed RNA-sequencing in order to profile KR jejunal transcriptome and to identify the transcriptional variations and biological pathways implied in response to divergent FCR. The biological pathways involved were revealed by enrichment of the Gene Ontology (GO) terms, and the Kyoto Encyclopedia of Gene and Genome (KEGG) pathways. The results showed that main pathways involved in KR FCR divergence were related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and maturation, development and growth. This is the first study to investigate the molecular genetic mechanisms affecting the FCR values in jejunum of slow-growing chicken. This study will be useful in the line-breeding programs for slow growing chickens to improve FE in the stockbreeding and its profitability.

overall_design: Jejunal samples of six KR were collected with extremely low FCR (n = 3) and high FCR (n = 3) and differentially expressed genes were identifiled using RNA-sequencing.

first: Cindy

last: Riou

first: Satoshi

last: Kubota

first: Chotima

last: Poompramun

first: Wittawat

last: Molee

first: Amonrat


title: Evaluation of the potential toxicity mechanism of single and combined exposure of dibutyl phthalate and diisobutyl phthalate to zebrafish (Danio rerio) testis based on transcriptomic analysis

city: Zhenjiang

first: Hui

last: Chen

address: Xuefu Road

institute: jiangsu university

summary: Aquatic organisms are generally exposed to a mixture of phthalate esters (PAEs) that have been shown to induce reproductive toxicity. However, their potential toxicity mechanisms to aquatic organisms remain unclear. Here male zebrafish were exposed to dibutyl phthalate (DBP), diisobutyl phthalate (DiBP) and their mixtures for 30 days, and their effects on plasma sex hormones, testis histology and testis transcriptomics were investigated. DBP, DiBP and their mixtures could induce the disequilibrating ratio of testosterone (T) and plasma estradiol (E2) in plasma. The percentage of spermatozoa (Sz) was significantly decreased by 30.6% under DBP-1133 exposure and 27.8% under Mix-3 exposure, and widen intercellular spaces appeared under DiBP-1038 exposure. Transcriptome sequencing revealed 2795 differentially expressed genes (DEGs) in the DBP-1133 exposure group, 1613 DEGs in the DiBP-1038 exposure group and 4570 DEGs in the Mix-3 exposure group, indicating that the toxicity of combined exposure was higher than that of single exposure. Cytokine-cytokine receptor interaction was associated with the toxicity mechanism of DBP, DiBP and Mix. While GnRH signaling pathway and MAPK signaling pathway were related to the toxicity mechanism of DBP. ECM-receptor interaction, steroid hormone biosynthesis, retinol metabolism and PPAR signaling pathway were associated with the toxicity mechanism of DiBP and Mix.

overall_design: Testis mRNA sequencing of adult female zebrafish after single and combined exposure to DBP and DiBP for 30 days

first: Weiwei

last: Feng

first: Kun

first: Xuchun

last: Qiu

first: Hai

last: Xu

first: Guanghua

last: Mao

first: Ting

last: Zhao

first: Yangyang

last: Ding

first: Xiangyang

last: Wu


title: Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance [Hi-C]

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

summary: Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. This study conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. We found that chromatin domains and looping genes’ strength have drastically changed during the 3D culture growth, although we identified very similar numbers of TADs and looping genes. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected Hippo relevant pathways genes with enhanced looping in breast cancer patient tissues’ organoid. Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer.

overall_design: Hi-C experiment of 3 cell types in 3D spheroids, 2 biological replicates for each cell type.

first: Jingwei

last: Li

first: Lavanya

last: Choppavarapu


title: Ablation of liver Fxr results in an increased colonic mucus barrier in mice

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

summary: The inter-organ cross talk between liver and intestine has been focus of intense research. Key in this cross-talk are bile acids, which are secreted from the liver into the intestine and, via the enterohepatic circulation, reach back to the liver. Important new insights have been gained in the Farnesoid X receptor (Fxr)-mediated communication from intestine-to-liver in health and disease. However, liver-to-intestine communication and the role of bile acids and FXR in this cross talk remain elusive. Here, we analyse Fxr-mediated liver-to-gut communication, and its consequences in the colon. Mice in which Fxr was selectively ablated in intestine (Fxr-intKO), the liver (Fxr-livKO), or in the full body (Fxr-totKO) were engineered. The effects on colonic gene expression (RNA sequencing), on the microbiome (16S rRNA Gene Sequencing) and on mucus barrier were analyzed. Compared to Fxr-intKO and Fxr-totKO mice, more genes were differentially expressed in the colons of Fxr-livKO mice relative to control mice (731, 1824 and 3272 respectively), suggestive of a strong role of hepatic Fxr in liver-to-gut communication. The colons of Fxr-livKO showed increased expression of anti-microbial genes, such as Regenerating islet-derived 3 beta and gamma (Reg3β and Reg3γ), Toll-like receptors (Tlrs), inflammasome related genes and  differential expression of genes belonging to the ‘Mucin-type O-glycan biosynthesis’ pathway. Compared to control mice, Fxr-livKO mice have decreased levels of the predicted mucin degrading bacterium Turicibacter and a concomitant increase in the thickness of the inner sterile mucus layer. In conclusion, ablation of Fxr in the liver has a major effect on colonic gene expression, the gut microbiome and on the permeability of the mucus layer. This stresses the importance of the Fxr-mediated liver-to-gut signaling.

overall_design: Mice in which Fxr was ablated in the intestine (Fxr-intKO), the liver (Fxr-livKO), or in full body (Fxr-totKO) were engineered. Fxr-floxed mice were used as controls. Colon tissue of 3 mice per group were used to evaluate changes in gene expression derived from selective Fxr ablation.

first: Jose

middle: M

first: Noortje

last: Ijssennagger

first: Saskia

middle: W

last: van Mil


title: Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice [exp2]

status: Public on Sep 27 2021

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

summary: RNA-sequencing data of female lumbar dorsal horn spinal cord microglia from WT or Treg KO mice after 3 days of CSF1 i.t. injection.

overall_design: FACS-microglia were collected, RNA was isolated and libraries were prepared using Nugen Trio RNA-seq kit and sequenced on Illumina HiSeq4000.

middle: D

first: Julia

middle: A

last: Kuhn

first: Allan

middle: I

last: Basbaum

first: Anna

middle: V

last: Molofsky


title: Transcriptomic response dynamics of human primary and immortalized adrenocortical cells to ACTH and Angiotensin II

city: NEW YORK

first: RUI

last: FU

state: NY

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

summary: RNA sequencing provides a transcriptome-wide view of what processes are activated and repressed during steroidogenesis. Here we performed an RNA-seq time series on primary human adrenocortical cells and H295R cells stimulated with ACTH or AngII (forskolin for H295R). We found that the ligand-induced changes in gene expression largely involved the same genes and similar timing. While stimulus-induced expression changes in H295R cells are recapitulated by primary cells, there are also expression changes unique to primary cells.

overall_design: RNA sequencing of forskolin-treated H295R cells and AngII/ACTH-treated primary adrenocortical cells

first: Neelanjan

last: Mukherjee

first: Kimberly

last: Wellman

first: Rui

last: Fu

first: Amber

last: Baldwin


title: Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice


title: Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice [exp1]

summary: RNA-sequencing data of male and female lumbar dorsal horn spinal cord microglia after 3 days of CSF1 or saline i.t. injection.

overall_design: FACS-microglia were collected, RNA was isolated and libraries were prepared using Nugen Ovation RNASeq System V2 kit and sequenced on Illumina HiSeq4000.


title: Transcriptional profiling of mouse neutrophils treated ex vivo with a Toll-like receptor 5 agonist

city: Buffalo

first: Andrei

last: Gudkov

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

summary: Acute radiation syndrome (ARS) is a major cause of lethality following radiation disasters. A TLR5 agonist, entolimod, is among the most powerful experimental radiation countermeasures and shows efficacy in rodents and non-human primates as a prophylactic (radioprotection) and treatment (radiomitigation) modality. While the prophylactic activity of entolimod has been connected to suppression of radiation-induced apoptosis, the mechanism by which entolimod functions as a radiomitigator remains poorly understood. Here, we demonstrate that, in contrast to radioprotection, neutrophils are essential for the radiomitigative activity of entolimod. We found that neutrophils express functional TLR5 and stimulation by entolimod is a key component to the mechanism of radiomitigation. Given that the underlying effects of TLR5 agonists have been associated with NF-kB-dependent transcriptional events, we hypothesized that changes in the transcriptional profile of neutrophils post-entolimod treatment mitigates radiation damage. However, RNA sequencing data analysis showed that ex vivo stimulation of neutrophils with entolimod for 30 minutes caused changes in transcriptional profiles that were substantially weaker – both in the number of responsive genes and scale of changes – as compared with that of liver cells following in vivo entolimod treatment. These observations suggest that mitigation of radiation damage by entolimod-stimulated neutrophils involves a transcriptional-independent mechanism.

overall_design: Gene expression profiles were generated by deep sequencing of neutrophils 30 minutes after ex vivo treatment with vehicle or entolimod. Neutrophils were magnetically isolated from the bone marrow of BALB/c mice. All experiments were performed in duplicate.

first: Craig

last: Brackett

first: Ivan

last: Molodtsov


title: The NF-κB transcriptional footprint is essential for SARS-CoV-2 replication

status: Public on Sep 28 2021

city: Hannover

first: Benjamin

middle: Erik

last: Nilsson-Payant

address: Feodor-Lynen-Straße 7

department: Experimental Virology

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Research

summary: SARS-CoV-2, the etiological agent of COVID-19, is characterized by a delay in Type I interferon (IFN-I)-mediated antiviral defenses alongside robust cytokine production. Here we investigate the underlying molecular basis for this imbalance and implicate virus-mediated activation of NF-κB in the absence of other canonical IFN-I-related transcription factors. Epigenetic and single cell transcriptomic analyses show a selective NF-κB signature that was most prominent in infected cells. Disruption of NF-κB signaling through the silencing of the NF-κB transcription factors p65 or p50 resulted in loss of virus replication that was rescued upon reconstitution. These findings could be further corroborated with the use of NF-κB inhibitors, which reduced SARS-CoV-2 replication in vitro. These data suggest that the robust cytokine production in response to SARS-CoV-2, despite a diminished IFN-I response, is the product of a dependency on NF-κB for viral replication.

overall_design: (1) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2  infected with SARS-CoV-2 (USA-WA1/2020, MOI: 2) for 2/4/6/9/12/18/24 hours. Samples were examined by mRNA-seq.   (2) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2  infected with SARS-CoV-2 (USA-WA1/2020, MOI: 0.01) for 24 hours. Samples were examined by scRNA-seq.   (3) Independent biological triplicates of transformed lung alveolar (A549) cells transduced with a vector expressing human ACE2  infected with SARS-CoV-2 (USA-WA1/2020, MOI: 0.1) for 24 hours. Samples were examined by ATAC-seq.

middle: E

first: Skyler

last: Uhl

first: Adrien

last: Grimont

first: Ashley

middle: S

last: Doane

first: Phillip

last: Cohen

first: Roosheel

last: Patel

first: Christina

last: Higgins

first: Joshua

last: Acklin

first: Yaron

last: Bram

first: Vasuretha

last: Chandar

first: Daniel

last: Blanco-Melo

first: Maryline

last: Panis

first: Jean

last: Lim

first: Olivier

last: Elemento

first: Robert

last: Schwartz

first: Brad

middle: R

last: Rosenberg

first: Rohit

last: Chandwani

last: tenOever


title: Blood transcriptomes of anti-SARS-CoV2 antibody  positive healthy individuals with prior  asymptomatic versus clinical infection

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

summary: Despite tremendous efforts by the international research community to understand the  pathophysiology of SARS-CoV-2 infection, the reasons behind the clinical variability, ranging from  asymptomatic infection to lethal disease, are still unclear. Existing inter-individual variations of the  immune responses, due to environmental exposures and genetic factors, may be critical to the  development or not of symptomatic disease after infection with SARS-CoV-2, and transcriptomic  differences marking such responses may be observed even later, after convalescence. Herein, we  performed genome-wide transcriptional whole-blood profiling to test the hypothesis that immune  response-related gene signatures may differ between healthy individuals with prior entirely  asymptomatic versus clinical SARS-CoV-2 infection, all of which developed an equally robust  antibody response. Among 12.789 protein-coding genes analyzed, there were only six and nine  genes with significantly decreased or increased expression, respectively, in those with prior  asymptomatic infection (n=17, mean age 34 years) relatively to those with clinical infection (n=15,  mean age 37 years). All six genes with decreased expression (IFIT3, IFI44L, RSAD2, FOLR3, PI3,  ALOX15), are involved in innate immune response while the first two are interferon-induced  proteins. Among genes with increased expression six are involved in immune response (GZMH,  CLEC1B, CLEC12A), viral mRNA translation (GCAT), energy metabolism (CACNA2D2) and  oxidative stress response (ENC1). Notably, 8/15 differentially expressed genes are regulated by  interferons. Our results suggest that an intrinsically weaker expression of some innate immunityrelated  genes may be associated with an asymptomatic disease course in SARS-CoV-2 infection.  Whether a certain gene signature predicts, or not, those who will develop a more efficient immune  response upon exposure to SARS-CoV-2, with implications for prioritization for vaccination,  warrant further study.

overall_design: 32 human whole blood samples of anti-SARS-CoV2 antibody positive healthy individuals with prior asymptomatic (n=17) versus clinical infection (n=15)

first: Petros

middle: P

last: Sfikakis

first: Kleio-Maria

last: Verrou

first: Ourania

last: Tsitsilonis

first: Dimitrios

last: Paraskevis

first: Efstathios

last: Kastritis

first: Evi

last: Lianidou

first: Paraskevi

last: Moutsatsou

first: Evangelos

last: Terpos

first: Ioannis

last: Trougakos

first: Vasiliki

last: Chini

first: Menelaos

last: Manoloukos

first: Panagiotis

last: Moulos

first: Georgios

last: Pavlopoulos

first: George

last: Kollias

first: Giannis

last: Ampatziadis-Michailidis

first: Pantelis

last: Hatzis

first: Meletios

last: Dimopoulos


title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University


title: ATAC seq from EGFP+ and EGFP- cells from postnatal day 3 striatum from GENSAT Nr4a1-EGFP mice

city: New York

first: Panos

last: Roussos

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: EGFP+ and EGFP- cells were sorted from dissected striatum from PND3 GENSAT Nr4a1-EGFP mice.

overall_design: In these mice, EGFP is expressed in the striatal striosome compartment, allowing for the identification of open chromatin regions in striosome and presumably matrix striatal compartments

first: John

middle: F

last: Fullard

first: Pasha

last: Apontes

first: Maria-Daniela

last: Cirnaru

first: Michelle

last: Ehrlich


title: Identification and validation of transcription factors and open chromatin regions defining the early postnatal striatal striosome

status: Public on Sep 26 2021

city: Novato

first: Lisa

last: Ellerby

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: The basal ganglia, best known for processing information required for initiation of movement, is also part of a network which regulates other aspects of movement, reward, and cognition. The major output nucleus of the basal ganglia is the striatum, and its functions are dependent on neuronal compartmentation, including into striosomes and matrix. Striatal projection neurons are GABAergic medium spiny neurons (MSNs), all of which share basic molecular signatures but are subtyped by selective expression of receptors, neuropeptides, and other gene families. Neurogenesis of the striosome and matrix occurs in separate waves, but the factors regulating terminal neuronal differentiation following migration are largely unidentified. We performed RNA- and ATAC-seq on sorted murine striosome and matrix cells at postnatal day 3 and with a focus on the striosomal compartment, validated the localization and/or role of transcription factors and their regulator(s), previously not known to be associated with striatal development, including Irx1, Foxf2, Olig2 and Stat1. In addition, we validated the enhancer function of a striosome-specific open chromatin region located 15Kb downstream of the Olig2 gene. These data and the data bases provide novel tools to dissect the networks regulating MSN compartmentation and differentiation and thus pathways relevant to movement and cognition.

overall_design: RNA-Seq analysis of the mouse straitum of 6 Nr4a1-EGFP positive and 6 Nr4a1-EGFP negative samples extracted from 6 different mice. Each sample has two technical replicate. 10 ng of total RNA was used for RNA-seq library preparation using the standard protocol from Takara Clontech Laboratories SMARTer Stranded Total RNA-Seq Pico Kit (Cat#635005 Clontech).150x2 bp paired-end RNA-seq reads were generated on a HiSeq 4000 sequencer.

first: Sean

last: Mooney

first: Sicheng

last: Song


title: Chromatin states and genomic organization impact replication timing and local patterns [ATAC-seq]

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Replication timing (RT) associates with genome architecture, while having a mixed relationship to histone marks.  By profiling replication at high-resolution and systematically assessing broad and focused histone marks across cell cycle with and without genetic perturbation, we address the causal relationship between histone marks, their associated states and RT. Our approach identified four chromatin states, including a previously uncharacterized H3K36me2 state, that defined 97% of the mappable genome. RT and local replication patterns (e.g., initiation zones) quantitatively associate with chromatin states, histone mark dynamics, and spatial chromatin structure. Furthermore, overexpression of the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT genome-wide (11%), which is linked to KDM4A-associated histone marks and clusters of enhancer elements.  Lastly, replication within H3K36me2-enriched neighborhoods is sensitive to KDM4A overexpression and is controlled at a megabase-scale.  These studies establish a critical role for chromatin regulation in regulating RT and the local RT patterns.

overall_design: Examination of replication timing in a replicate of RPE control or stably overexpressing KDM4A, at seven phases of cell cycle: ES, LS, G2/M, S1, S2, S3, S4

first: Johntahan

last: Whetstine

first: Ruslan

last: Sadreyev

first: Capucine

last: van Rechem


title: Chromatin states and genomic organization impact local replication features and timing


title: Chromatin states and genomic organization impact local replication features and timing [ChIP-seq]

summary: Replication timing (RT) control is linked to histone modifications (HMs) and genome architecture. However, HM landscape across cell cycle and its relationship with RT and chromatin modifiers have not been comprehensively assessed. Here we perform detailed replication profiling together with cell cycle profiling of multiple HMs, ATAC-seq, and gene expression. We classify 97% of the genome into four gross chromatin states, including a previously uncharacterized intergenic H3K36me2 state. RT and associated replication features (e.g. initiation zones) quantitatively associate with these chromatin states, HM dynamics, and spatial chromatin structure. Furthermore, overexpression of the histone H3 lysine 9/36 tri-demethylase KDM4A impacts RT across 12% of the genome.  RT regulation is strongly linked to KDM4A-associated HMs and enhancer-like elements.  Lastly, replication within the intergenic H3K36me2 neighborhoods is sensitive to KDM4A overexpression and is controlled as wide megabase-scale units.  In conclusion, these studies establish a critical role for chromatin regulation in directing RT genome-wide.


title: Screening bioactive food compounds in honey bees suggests curcumin blocks alcohol-induced damage to longevity and DNA methylation

city: Aas

first: Erik

middle: Magne Koscielniak

last: Rasmussen

address: Universitetstunet 3

country: Norway

institute: Norwegian University of Life Sciences

type: Methylation profiling by high throughput sequencing

summary: Various bioactive food compounds may confer health and longevity benefits, possibly through altering or preserving the human epigenome. While bioactive food compounds are widely being marketed as ‘improving health and longevity’ by counteracting harmful effects of poor nutrition and lifestyle, claimed effects are often not adequately documented. Using the honey bee (Apis mellifera) as a model species, we here employed a multi-step screening approach to investigate seven compounds for effects on lifespan and DNA methylation using ELISA and whole genome bisulfite sequencing (WGBS). A positive longevity effect was detected for valproic acid, isovaleric acid, and cyanocobalamin. For curcumin, we found that lifespan shortening caused by ethanol intake, was restored when curcumin and ethanol were co-administered. Furthermore, we identified region specific DNA methylation changes as a result of ethanol intake. Ethanol specific changes in DNA methylation were fully or partially blocked in honey bees receiving ethanol and curcumin together. Ethanol-affected and curcumin-blocked differentially methylated regions covered genes involved in fertility, temperature regulation and tubulin transport. Our results demonstrate fundamental negative effects of low dose ethanol consumption on lifespan and associated DNA methylation changes and present a proof-of-principle on how longevity and DNA methylation changes can be negated by the bioactive food component curcumin. Our findings provide a fundament for further studies of curcumin in mice and humans and offer an avenue to explore regarding possible prevention of health issues related to alcohol consumption.

overall_design: Investigation of differentialy methylated regions in honey bees receiving ethanol and ethanol combined with curucmin in diet

first: Kristine

middle: L

last: Seier

first: Ingrid

middle: K

last: Pedersen

first: Claus

last: Kreibich

first: Gro

last: Amdam

first: Daniel

last: Münch

first: John Arne

last: Dahl


title: Histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development

status: Public on Sep 25 2021

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Analysis of the transcriptional profiles of developing thymocytes has shown that T lineage commitment is associated with loss of stem cell and early progenitor gene signatures and the acquisition of T cell gene signatures. Less well understood are the epigenetic alterations that accompany or enable these transcriptional changes. Here, we show that the histone demethylase Lsd1 (Kdm1a) performs a key role in extinguishing stem/progenitor transcriptional programs in addition to key repressive gene programs during thymocyte maturation. Deletion of Lsd1 caused a block in late T cell development and resulted in overexpression of interferon response genes as well as genes regulated by the Gfi1, Bcl6, and, most prominently, Bcl11b transcriptional repressors in CD4+CD8+ thymocytes. Transcriptional overexpression in Lsd1-deficient thymocytes was not always associated with increased H3K4 trimethylation at gene promoters, indicating that Lsd1 indirectly affects the expression of many genes. Together, these results identify a critical function for Lsd1 in the epigenetic regulation of multiple repressive gene signatures during T cell development.

overall_design:
RNA-Seq: 2 genotypes (Lsd1-KO, WT) x 2 conditions (CD69-, CD69+) x 4 biological replicates = 16 samples (x 2 technical replicates).
ChIP-Seq:
1) H3K4me1 - 2 genotypes (Lsd1-ko, WT) x 2 biological replicates = 4 IP samples (x 2 technical replicates) + 2 input (Lsd1-KO, WT).
2) H3K4me2 - 2 genotypes (Lsd1-KO, WT) x 2 biological replicates = 4 IP samples + 4 input samples (Lsd1-KO, WT x 2 replicates).
3) H3K4me3 - 2 genotypes (Lsd1-KO, WT) x 3 biological replicates = 6 IP samples + 2 input (Lsd1-KO, WT) = 22 samples.
scRNA-Seq: 2 genotypes (Lsd1 fl/fl, CD2-iCre; Lsd1 fl/fl) x 2 biological replicates = 4 samples.

middle: B

last: Stamos

first: Lauren

middle: M

last: Clubb

first: Laura

last: Chopp

first: Jie

last: Nie

first: Yi

last: Ding

first: Arundhoti

last: Das

first: Harini

last: Venkataganesh

first: Jan

last: Lee

first: Dalal

last: El-Khoury

first: LiQi

last: Li

first: Avinash

last: Bhandoola

first: Remy

last: Bosselut

first: Paul

last: Love


title: Chromatin states and genomic organization impact local replication features and timing [Repli-seq]

first: Fei

last: Ji

first: Johntahan

last: Whetstine

first: Ruslan

last: Sadreyev

first: Capucine

last: van Rechem


title: Selective extracellular signSelective Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibition by the SCH772984 Compound Attenuates In Vitro and In Vivo Inflammatory Responses and Prolongs Survival in Murine Sepsis Models

status: Public on Sep 24 2021

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Sepsis is the leading cause of death in intensive care units worldwide. Current treatments of sepsis are largely supportive and clinical trials using specific pharmacotherapy for sepsis have failed to improve outcomes. Here, we used the lipopolysaccharide (LPS)-stimulated mouse RAW264.7 cell line and AlphaLisa assay for TNFa as a readout to perform a supervised drug repurposing screen for sepsis treatment with compounds targeting epigenetic enzymes, including kinases. We identified the SCH772984 compound, an extracellular signal-regulated kinase (ERK) 1/2 inhibitor, as an effective blocker of TNFa production in vitro. RNA-Seq of the SCH772984-treated RAW264.7 cells at 1, 4, and 24 h time points of LPS challenge followed by functional annotation of differentially expressed genes highlighted the suppression of cellular pathways related to the immune system. SCH772984 treatment improved survival in the LPS-induced lethal endotoxemia and cecal ligation and puncture (CLP) mouse models of sepsis, and reduced plasma levels of Ccl2/Mcp1. Functional analyses of RNA-seq datasets for kidney, lung, liver, and heart tissues from SCH772984-treated animals collected at 6 h and 12 h post-CLP revealed a significant downregulation of pathways related to the immune response and platelets activation but upregulation of the extracellular matrix organization and retinoic acid signaling pathways. Thus, this study defined transcriptome signatures of SCH772984 action in vitro and in vivo, an agent that has the potential to improve sepsis outcome

overall_design: Lung, kidney, liver and heart tissues collected from four animals in CLP, CLP+ SCH772984 and sham group at 6h and 12h time points post-CLP were subjected to RNA-Seq. Sets of organs are matching same animals in a given group. The in vitro experiment was performed on three independent biological replicates per treatment. In sum 80 tissue and 24 cell culture samples are included.

first: Michał

last: Kopczyński

first: Izabela

last: Rumieńczyk

first: Maria

last: Kulecka

first: Małgorzata

last: Statkiewicz

first: Kazimiera

last: Pyśniak

first: Zuzanna

last: Sandowska-Markiewicz

first: Urszula

last: Wójcik-Trechcińska

first: Krzysztof

last: Goryca

first: Karolina

last: Pyziak

first: Eliza

last: Majewska

first: Magdalena

last: Masiejczyk

first: Katarzyna

last: Wójcik

first: Tomasz

last: Rzymski

first: Karol

last: Bomsztyk

first: Jerzy

last: Ostrowski


title: CSC-derived Cardiomyocytes Exhibit the Typical microRNA-mRNA Blueprint of Adult Cardiomyocytes

city: Catanzaro

first: Daniele

last: Torella

state: Catanzaro

address: Viale Europa, loc. Germaneto

department: Experimental and clinical medicine

country: Italy

institute: University "Magna Graecia"

summary: We addressed here whether cardiomyocytes generated from CSC differentiation in vitro (iCMs) have a similar pattern of gene expression and undergo a similar transcriptional switch typical of cell cycle exit during adult cardiac myocyte maturation through the activation of known myo-miRs.

overall_design: RNA-seq data from CSCs, iCMs and aCMs isolated from wt mice have been analysed and compared.

first: Mariangela

last: Scalise

first: Fabiola

last: Marino

first: Luca

last: Salerno

first: Teresa

last: Mancuso

first: Donato

last: Cappetta

first: Antonella

last: Barone

first: Elvira

last: Parrotta

first: Annalaura

first: Domenico

last: Palumbo

first: Pierangelo

last: Veltri

last: De Angelis

first: Liberato

last: Berrino

first: Francesco

last: Rossi

first: Alessandro

last: Weisz

first: Marcello

last: Rota

first: Konrad

last: Urbanek

first: Eleonora

last: Cianflone


title: Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

summary:
Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentiation and X inactivation by integrating, for the first time, allele-specific data obtained by high-throughput single-cell RNA-seq, ATAC-seq, and Hi-C. In differentiated cells, contact decay profiles, which clearly distinguish the active and inactive X chromosomes, reveal loss of the inactive X-specific structure at mitosis followed by a rapid reappearance, suggesting a bookkeeping mechanism. In differentiating embryonic stem cells, changes in contact decay profiles are detected in parallel on both the X chromosomes and autosomes, suggesting profound simultaneous reorganization. The onset of the inactive X-specific structure in single cells is notably delayed relative to that of gene silencing, consistent with the idea that chromatin compaction is a late event of X inactivation. Novel computational approaches to effectively align single-cell gene expression, chromatin accessibility, and 3D chromosome structure reveal that long-range structural changes to chromosomes appear as discrete events, unlike progressive changes in gene expression and chromatin accessibility.

### Competing Interest Statement

The authors have declared no competing interest.

### This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genetic regulator of mitochondrial metabolism and insulin resistance [ncRNA-Seq]

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

institute: The Kids Research Institute Australia

summary: Mitochondrial energy metabolism and function are key processes underlying the pathophysiology of insulin resistance and predisposition to type 2 diabetes. This is because mitochondria produce most of the energy required by the cell. Impaired energy production, use of energy stores and mitochondrial dysfunction are major features in metabolic diseases. Nevertheless, it remains uncertain how mitochondrial dysfunction can cause, contribute to, or result in insulin resistance and metabolic diseases. Furthermore there is growing evidence from genetic and genome wide-association studies that genetic variation in mtDNA contributes to these common metabolic diseases (Wallace, 2005), however there has been essentially no in vivo functional validation for these findings. Therefore we generated a mouse model homozygous for a polymorphism in the Mrpp3 gene identified in the French Canadian population responsible for 22% of mitochondrial epitranscriptome variation, with likely consequences on metabolism. We investigated the in vivo effects of the polymorphism on mitochondrial function and metabolism in mice fed normal and high fat diet. We identify that the polymorphism reduces the efficiency of mitochondrial RNA processing and this is most pronounced in the pancreas that results in insulin resistance. The MRPP3 protein containing the Asn434Ser polymorphism associates specifically with the calcium antiporter LETM1 preventing effective release of calcium from mitochondria and consequently impairs insulin release from the pancreatic islet cells of these mice. Reduction in insulin secretion and enlarged pancreatic islet size results in lower circulating levels of insulin that causes insulin resistance and liver steatosis. Our findings reveal for the first time the link between mitochondrial gene regulation and insulin resistance via calcium signaling.

overall_design: Small RNA coverage and analysis of tRNA position 9 mismatch rates of pancreatic RNA isolated from three Mrpp3WT and three Mrpp3N434S mice fed on a high-fat diet.

first: Giulia

last: Rossetti

first: Tara

last: Richman

first: Kara

last: Perks

first: Laetitia

last: Hughes

first: Judith

last: Ermer

first: Emma

last: Jameison

first: Nicola

last: Ferreira

first: Anne-Marie

last: Shearwood

first: Natalie

middle: C

last: Ward

first: Helena

last: Viola

first: Livia

last: Hool

first: Dusanka

last: Milenkovic

first: Nils-Göran

last: Larsson

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Genetic regulator of mitochondrial metabolism and insulin resistance

summary: This SuperSeries is composed of the SubSeries listed below.


title: Multi-Omics Approaches Explain the Growth-Promoting Effect of the Apocarotenoid Growth Regulator Zaxinone in Rice

status: Public on Sep 23 2021

city: Thuwal

first: Jian You

last: Wang

state: Not Specified

address: 4700 King Abdullah University of Science and Technology (KAUST) Thuwal, 23955-6900, Kingdom of Saudi Arabia

country: Saudi Arabia

institute: KAUST

summary: The apocarotenoid zaxinone promotes growth and suppresses strigolactone biosynthesis in rice. To shed light on the mechanisms underlying its growth promoting effect, we employed a combined omics approach integrating transcriptomics and metabolomics analysis of rice seedlings treated with zaxinone

overall_design: Examination of zaxinone effect on rice seedlings

first: Salim

last: Al-Babili

first: Abdugaffor

last: Ablazov


title: Genetic regulator of mitochondrial metabolism and insulin resistance [RNA-Seq]

first: Stefan

last: Siira

overall_design: RNA sequencing and mitochondrial coverage analysis of total pancreatic RNA isolated from three Mrpp3WT and three Mrpp3N434S mice fed on a normal chow diet and a high-fat diet.

first: Giulia

last: Rossetti

first: Tara

last: Richman

middle: A


title: Selective Extracellular Signal-Regulated Kinase 1/2 (ERK1/2) Inhibition by the SCH772984 Compound Attenuates In Vitro and In Vivo Inflammatory Responses and Prolongs Survival in Murine Sepsis Models

first: Michal

last: Mikula

summary: This is an accompanying ATAC-seq data to the transcriptomic survey of RAW264.7 cells treated with ERK1/2 inhibitor SCH772984 upon 1hr, 4hrs and 24 hrs LPS challenge. The transcriptomic data are deposited in GEO under GSE179554.

overall_design: The experiment was performed on two independent biological replicates per treatment. 16 samples are included.

first: Michał

last: Kopczyński

first: Izabela

last: Rumieńczyk

first: Maria

last: Kulecka

first: Małgorzata

last: Statkiewicz


title: Analysis of cellular heterogeneity in immune microenvironment of Primary central nervous system lymphoma by single cell sequencing

city: Hong Kong

first: Zhe

last: LIU

address: Tat Chee Avenue

department: computer science

institute: city university of hong kong

summary: Human PCNSL tumor samples were obtained surgically from clinical patients confirmed by pathology from our hospital. After sample collection processing and suspensions, we performed scRNA-seq following the manufacturer’s protocol. Briefly, the cells were washed with PBS and resuspended in 500 μl PBS. scRNA-seq libraries were prepared using a Chromium Single cell 3’ Reagent kit, version 2. Amplified cDNA and final libraries were evaluated using a High Sensitivity DNA Kit (Agilent Technologies). Sequencing was performed on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads.

overall_design: The Cell Ranger software pipeline (version 4.0, http://support.10Xgenomics.com/single-cell-gene-expression/software/overview/welcome) provided by 10x Genomics was used to demultiplex cellular barcodes. Unique molecular identifier (UMI) counts were obtained by mapping reads to the human reference genome (GRCH38 3.1.0) genome and align transcriptomes using the STAR aligner and down-sample reads as required to generate normalized aggregate data across samples. In the end, a matrix of gene counts by cells was produced. We processed the UMI count matrix using the Seurat R package (version 4.0.2), resulting in 34,851 cells with 36,601 genes for PCNSL samples.  We first removed the likely multiplet captures which is a major concern in microdroplet-base experiments through doubletfinder. We filtered cells at the cell and gene levels to obtain the reliability results of PCNSL scRNA-seq data, respectively. We removed the low qualify cells with the following criteria: (i) The number of expressed genes was <200 or >2,000; (ii) The number of total counts was > 20,000. (iii) The percentage of mitochondrial counts > 10%. We only kept the genes detected in at least 20 cells. After applying these quality control criteria, we obtained 20,307 cells with 12,229 genes in total, which were used for downstream analysis.  Similar to normal CNS scRNA-seq data, we used the following criteria: (i) The number of expressed genes was <100 or >3,000; (ii) The number of total counts was > 20,000. (iii) The percentage of mitochondrial counts > 10%. We only kept the genes detected in at least 20 cells. After applying these quality control criteria, we obtained 20,015 cells with 16,608 genes from 21,255 cells with 33,694 genes in total, which were used for downstream analysis.

first: Boyuan

last: Wei

last: Liu

first: Gang

last: Cheng

first: Jianning

last: Zhang


title: Effect of certain microorganisms on mouse gut microbial communities.

city: Gyeonggi-do

first: Jisoo

last: Kim

address: 22, Giheungdanji-ro 24beon-gil, Giheung-gu, Yongin-si

department: New growth team

country: South Korea

institute: hy R&BD center

summary: Effect of certain microorganisms on mouse gut microbial communities in aged group.

overall_design: Cecal samples were collected from each mouse and metagenomic analysis was conducted.

first: Kippeum

last: Lee


title: Host response transcriptomic analysis of Crimean-Congo hemorrhagic fever pathogenesis in the cynomolgus macaque model

city: Frederick

first: Catherine

last: Arnold

address: 1425 Porter St

department: Diagnostic Systems Division

institute: US Army Medical Research Institute of Infectious Diseases

summary: A NanoString targeted gene panel was used to elucidate the transcriptomic changes occurring in non-human primate whole blood during Crimean Congo Hemorrhagic Fever Virus infection.

overall_design: Twelve cynomolgus macaques were challenged with either Afghan09-2990 or Kosava Hoti strain at a target dose of 6 log10 PFU/mL.  Blood samples were collected on days 0, 1-7, 9, 12, 14, 21, and 28 for total RNA extraction and NanoString analysis using the nCounter NHP Immunology v2 Panel.

first: Charles

last: Shoemaker


title: Generation of a functional, patient specific human thymus from induced pluripotent stem cell in vivo

city: Aurora

first: Holger

last: Russ

state: CO

address: 1775 Aurora Ct

department: Barbara Davis Center for Diabetes

institute: University of Colorado Anschutz Medical Campus

summary: Here we describe a universal direct differentiation protocol that allows the generation of thymic epithelial progenitor cells (TEPs) from different iPSC lines. Upon transplantation into an athymic mouse model, TEPs further differentiate into thymic epithelial cells (TECs). TECs are functional and can facilitate the education of developing mouse T-cells. iPSC derived, patient specific TECs residing within grafts are indistinguishable from TECs present in human primary neonatal thymus tissue as revealed by single cell RNA sequencing analysis indicating the generation of a mature TEC phenotype. Taken together, we provide a universal direct differentiation protocol that generates TEPs from all iPSC lines tested, that can further differentiate into mature, functional TECs. We anticipate that these findings have important implications for current efforts aimed at generating a functional human thymus.

overall_design: Generatiion of a universal direct differentiation protocol for the generation of thymic epithelial progenitors from human iPSCs. Further, analysis of human iPSC derived thymic epithelial progenitors and in vivo matured thymic epithelial cells by single cell and bulk RNA sequencing.

first: Stephan

last: Ramos


title: Identification of WTAP complex-regulated alternative splicing/polyadenylation

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

institute: Institute for Advanced Medical Sciences, Nippon Medical School

summary: Through combined comprehensive analysis of AS events via RNAi, coupled with RNA-seq analysis, we demonstrate that the WTAP complex core factors WTAP, VIRMA, KIAA0853 and CBLL1 function as splicing regulators to promote exon skipping and intron retention, several of which occur in the last exon with competition between splicing and polyadenylation. The regulated alternative splicing (AS) events involve short introns/exons with higher GC content and introns with weaker polypyrimidine-tract and branch points. Further analysis of GC-rich sequences of WTAP-regulated AS events revealed potential G-quadruplex formation.

overall_design: Tranascriptome analysis of WTAP-complex knockdown Human Umbilical Vein Endothelial Cells (HUVECs)

first: Keiko

last: Horiuchi


title: Altered pattern of circulating miRNAs in HIV lipodystrophy perturbs key adipose differentiation and inflammation pathways

status: Public on Sep 22 2021

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: We identified a microRNA (miRNA) profile characterizing HIV lipodystrophy and explored the downstream mechanistic implications with respect to adipocyte biology and the associated clinical phenotype. Human preadipocytes transfected with mimic miR-20a-3p, anti–miR-324-5p, or anti–miR-186 induced consistent changes in latent transforming growth factor beta binding protein 2 (Ltbp2), Wisp2, and Nebl expression.

overall_design: Human preadipocytes were transfected with miR-20a-3p mimic, anti–miR-186, anti–miR-324-5p,or control nontargeting miRNA and then cultured in differentiation medium for 12 additional days to give rise to mature adipocytes, after which RNA was collected and subjected to RNA-Seq.

first: Suman

last: Srinivasa

first: Ruben

last: Garcia-Martin

first: C

last: Kahn

first: Steven

last: Grinspoon


title: Single-cell ATAC-seq of developing cortical interneurons.

city: Cambridge

first: Kathryn

last: Allaway

address: 75 Ames St

department: Stanley Center for Psychiatric Disease

institute: Broad Institute

summary: Single-cell ATAC-sequencing of cortical GABAergic interneurons to characterize the chromatin landscapes of these cells at several timepoints across development - from their origins in the ganglionic eminences, upon migration to the cortex, settling in cortical laminae, and through maturation.

overall_design: scATAC-seq libraries generated from E13 MGE, E14 CGE, E14 Cortex, E18 Dlx6a+ Cortex, P2 Dlx6a+ Cortex, P10 Dlx6a+ Cortex, P28 Dlx6a+ Cortex

first: Mariano

middle: I

last: Gabitto


title: Multiomic sequencing of the MGE

summary: Single-cell multiomic sequencing (RNA+ATAC in the same cells) of the E13.5 medial ganglionic eminence (MGE).

overall_design: Multiomic (RNA (gene expression)/ATAC (chromatin accessibility) libraries were generated for cells isolated from the E13.5 MGE using the 10X Genomics Multiome platform.


title: Single-cell RNA-seq of developing cortical interneurons

summary: Single-cell RNA-sequencing of cortical GABAergic interneurons to characterize their transcriptional profiles at several timepoints across development - from their origins in the ganglionic eminences, upon migration to the cortex, settling in cortical laminae, and through maturation.

overall_design: scRNA-seq libraries generated from E13 MGE, E14 CGE, P2 Dlx6a+ Cortex, P10 Dlx6a+ Cortex, P28 Dlx6a+ Cortex

first: Orly

last: Wapinski

first: Rachel

last: Bandler


title: Newly-Discovered Neural Features Expand the Pathobiological Knowledge of Blastic Plasmacytoid Dendritic Cell Neoplasm

status: Public on Sep 17 2021

city: MILAN

first: Maria Rosaria

last: Sapienza

state: Italy

address: Via Ripamonti, 435

department: Division of Haematopathology

institute: IEO, European Institute of Oncology IRCCS

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and highly aggressive hematologic malignancy originating from plasmacytoid dendritic cells (pDCs). The microRNA expression profile of BPDCN was compared to that of normal pDCs and the impact of miRNA dysregulation on the BPDCN transcriptional program was assessed. MiRNA and gene expression pro-filing data were integrated to obtain the BPDCN miRNA-regulatory network. The biological process mainly dysregulated by this network was predicted to be neurogenesis, a phenomenon raising growing interest in solid tumors. Neurogenesis was explored in BPDCN by querying different molecular sources (RNA sequencing, Chromatin immunoprecipitation-sequencing, and immunohistochemistry). It was shown that BPDCN cells upregulated neural mitogen genes possibly critical for tumor dissemination, expressed neuronal progenitor markers involved in cell migration, exchanged acetylcholine neurotransmitter, and overexpressed multiple neural re-ceptors that may stimulate tumor proliferation, migration and cross-talk with the nervous system. Most neural genes upregulated in BPDCN are currently investigated as therapeutic targets.

overall_design: In the study presented here, a cohort of 19 BPDCN tumor samples and 4 normal plasmacytoid dendritic cell samples (used as controls) was used to acquire the expression profile of 734 endogenous microRNAs..

first: Maria

first: Stefano

last: Pileri


title: Nanopore sequencing of K562 for DNA cytosine modification detection

status: Public on Sep 20 2021

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

summary: Nanopore sequencing of K562 human cell line using the Oxford Nanopore GridION and R9.4.1 version chemistry

overall_design: Genomic DNA from K562 was extracted and Nanopore sequencing was applied to detect DNA cytosine modification

first: Yang

last: Liu

first: Wojciech

last: Rosikiewicz

first: Ziwei

first: Nathaniel

last: Jillette

first: Albert

last: Cheng


title: Quinacrine induces nucleolar stress in treatment-refractory ovarian cancer

city: Sacramento

first: Dennis

last: Montoya

address: 2700 Stockton Blvd

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: A considerable subset of gynecologic cancer patients’ experiences disease recurrence or acquired resistance, which contributes to high mortality rates in ovarian cancer (OC). Our prior studies showed that quinacrine (QC), an antimalarial drug, enhanced chemotherapy sensitivity in treatment-refractory OC cells, including artificially generated chemoresistant and high-grade serous OC cells. In this study, we investigated QC-induced transcriptomic changes to uncover its cytotoxic mechanisms of action. Isogenic pairs of OC cells generated to be chemo-resistant and chemo-sensitive counterparts were treated with QC followed by RNAseq analysis. Validation of selected expression results and database comparison analyses indicated the ribosomal biogenesis (RBG) pathway is inhibited by QC. RBG is commonly upregulated in cancer cells and is emerging as a drug target. We found that QC attenuates the in vitro and in in vivo expression of nucleostemin (NS/GNL3), a nucleolar RBG and DNA repair protein, and the RPA194 catalytic subunit of Pol I that results in RBG inhibition and nucleolar stress. QC promotes the redistribution of fibrillarin in form of extranuclear foci and nucleolar caps, an indicator of nucleolar stress conditions. In addition, we found that QC-induced downregulation of NS disrupted homologous recombination repair both by reducing NS protein levels and parylation resulting in reduced RAD51 recruitment to DNA damage. Our data suggests that QC inhibits RBG and this inhibition promotes DNA damage by directly downregulating the NS-RAD51 interaction. Additionally, QC showed strong synergy with PARP inhibitors in OC cells. Overall, we found that QC by downregulates the RBG pathway, induces nucleolar stress, supports the increase of DNA damage, and sensitized cells to PARP inhibition, which supports new therapeutic stratagems for treatment-refractory OC. Our work offers support for targeting RBG in OC and determines NS to be a novel target for QC.

overall_design: Six hour treatment with quinacrine or control of cell lines that are sensitive or resistant to platinum chemotherapy.

first: Vijayalakshmi

last: Shridhar

first: Jeremy

last: Chien


title: Genome-wide localization of SUMO-modified proteins in untreated or heat-shocked budding yeast

status: Public on Sep 21 2021

city: Toronto

first: Emanuel

last: Rosonina

state: ON

address: 4700 Keele Street

department: Biology

institute: York University

summary: Most SUMO-modified proteins in budding yeast and human cells are associated with chromatin. To determine specifically where sumoylated proteins are found across the genome, we performed ChIP-seq with a SUMO antibody in budding yeast. We identified 603 loci that each contain a stable SUMO peak. In agreement with a previous study, most of these sites correspond to tRNA genes or genes that encode ribosomal proteins (RPGs). However, 147 of the SUMO peaks in our analysis are found at promoters of protein-coding genes that are not RPGs (non-RPGs), many of which are among the most highly expressed genes. By comparing our data with other ChIP-seq studies, we determined that non-RPG SUMO peaks are situated precisely where general transcription factors (GTFs) assemble, but not where RNA polymerase II (RNAPII) or other promoter-proximal proteins bind. In support of this, we determined that the large subunit of TFIIF is the major SUMO target among GTFs and propose that its sumoylation controls the dynamics of RNAPII gene association. Additionally, we found that exposing yeast to a brief heat shock significantly reduces the intensity of SUMO peaks at most genes of all classes, which likely reflects the vast transcriptional reprogramming that occurs in response to temperature stress.

overall_design: Two independent replicates of SUMO ChIP-seq were performed using normally growing or heat-shocked wild-type yeast and in the sumoylation-deficient ubc9-6 strain.

first: Benjamin

middle: G

last: Bergey

first: Marjan

last: Moallem


title: Nascent RNA sequencing (PRO-seq) after estrogen treatment in T47D cells

first: Michael

middle: Joseph

last: Guertin

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

summary: This experiment identifies the primary estrogen response genes in T47D cells.

overall_design: T47D cells were hormone starved for 3 days and then treated with estrogen or a vehicle control for 1 hour.

first: Thomas

last: Scott


title: MEF2C CUT&RUN in PV and SST interneurons.

first: Kathryn

last: Allaway

summary: CUT&RUN for MEF2C in mature PV+ and SST+ cortical interneurons to characterize the differential usage of this transcription factor by these populations.

overall_design: CUT&RUN against MEF2C in PV+ and SST+ cortical interneurons isolated from the mature cortex from PV-Cre;INTACT and SST-Cre;INTACT mice.

first: Chen-Yu

last: Wang

first: Mariano

last: Gabitto


title: Comparative analysis of glioblastoma initiating cells and patient-matched EPSC-derived neural stem cells as a discovery tool and drug matching strategy

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

type: Methylation profiling by genome tiling array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genetic and epigenetic coordination of cortical interneuron development


title: Comparative analysis of glioblastoma initiating cells and patient-matched EPSC-derived neural stem cells as a discovery tool and drug matching strategy [array]

summary: Malignant gliomas are the most common intrinsic brain tumors in adults and are associated with a very poor prognosis, which has not improved in the last 20 years. We show here that glioblastoma initiating cells (GIC) and syngeneic neural stem cells derived from enhanced pluripotent stem cells (iNSC) are a suitable novel pre-clinical pipeline to discover new patient-specific disease mechanisms and to identify druggable targets for personalized therapy.

overall_design: Methylation analysis of human dura mater fibroblasts, iPSC, iNSC, GIC and FFPE bulk tumor

first: Claire

last: Vinel

first: Gabriel

last: Rosser

first: Loredana

last: Guglielmi

first: Nicola

last: Pomella

first: Myrianni

last: Constantinou

first: Xinyu

last: Zhang

first: James

last: Boot

first: Tania

last: Jones

middle: O

last: Millner

first: Anaelle

last: Dumas

first: Vardhman

last: Rakyan

last: Rees

first: Yau

last: Lim

first: Jamie

last: Thompson

first: Juho

last: Vuononvirta

first: Tedani

last: El Assan

first: Natasha

last: Aley

first: Yung-Yao

last: Lin

first: Pentao

first: Denise

last: Sheer

first: Catherine

last: Merry

first: Federica

last: Marelli-Berg

first: Sebastian

last: Brandner


title: Genome-wide maps of acetylated lysine 27 of Histone 3 (ChIP-seq) and gene expression profiling (RNA-seq) in  wildtype and USP7-KO H1299 lung cancer lines

status: Public on Sep 16 2021

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: Ubiquitin Specific Protease 7 (USP7), also named as herpesvirus-associated ubiquitin-specific protease (HAUSP), is one of the most abundant deubiquitinase and plays multifaceted roles in many cellular functions, including the protein homeostasis, DNA repair, gene transcription, and oncogenic pathways. To investigate the role of USP7 in p53-deficient lung cancer cells, the CRISPR/Cas9-mediated gene editing was employed to inactivate the USP7 locus in H1299 cells. The alterations of transcriptional enhancers and gene expression were analyzed by H3K27ac ChIP-seq and RNA-seq, respectively, in wildtype and USP7-KO H1299 lung cancer cells.

overall_design: Genome-wide binding/occupancy profiling of H3K27ac by ChIP-seq  and gene expression profiling by RNA-seq in wildtype and USP7-KO H1299 lung cancer cells

first: Yu-Ting

last: Huang


title: RNA sequencing of mammary glands from 55-day old control, MTB-200ba429, MTB-IGFIR, MTB-IGFIRba429 mice.

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

summary: RNA was isolated from mammary glands from 55 day old control mice, mice overexpressing the miR-200b/200a/429 cluster in mammary epithelial cells (MTB-200ba429) mice overexpressing the IGF-IR transgene in mammary epithelial cells (MTB-IGFIR), and mice overexpressing both the miR-200b/200a/429 cluster and the IGF-IR transgene in mammary epithelial cells (MTB-IGFIRba429)

overall_design: 4 control, 4 MTB-200ba429, 4 MTB-IGFIR and 3 MTB-IGFIRba429 samples


title: Ad Libitum Feeding in Broiler Breeder Hens Alters Transcriptome of Granulosa Cells of Prehierarchal Follicles

city: Ithaca

first: Pat

last: Johnson

state: New York

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

summary: Intense selective breeding of broiler breeds of chickens has resulted in suboptimal egg production in broiler breeder hens. Ad libitum feeding which leads to excessive and disorganized follicular growth exacerbates this reproductive phenotype. One strategy used to improve broiler breeder hen reproductive efficiency is restricted feeding. In this study, we sought to identify transcriptional changes which translate level of dietary intake to increased follicle selection. Broiler breeder hens were raised according to commercial guidelines until 28 weeks of age and then randomly assigned to an ad libitum diet (FF) or continued on a restricted diet (RF) for 6 weeks. Following dietary treatment, granulosa cells from growing 6-8 mm follicles from FF hens (n=3) and RF hens (n=3) were collected, RNA was extracted, and samples were processed for RNA-sequencing on Illumina NextSeq 500. Transcriptomes of granulosa cells from 6-8 mm follicles were sequenced to identify transcriptional differences in the population from which follicles are selected into the preovulatory stage.  FastQ files were first processed through trim-galore and reads were aligned to the Galgal6 genome using the RNA-seq aligner, STAR. A cluster analysis using hclust in R identified a FF sample as an outlier and this sample was removed from the analysis. Differential expression analysis was conducted using DeSEQ2 and resulted in 350 differentially expressed genes. Several genes involved in follicle selection were upregulated in prehierarchal follicles of FF hens, suggesting an effect of dietary treatment at early stages in follicle development.

overall_design: Granulosa cells of 6-8 mm follicles mRNA profiles of 2 FF and 3 RF hens.

first: Laurie

last: Francoeur

first: Claire

middle: S

last: Stephens

first: Patricia


title: RNA-seq of four tissue samples of dedifferentiated liposarcoma and corresponding matched well-differentiated liposarcoma

city: Shanghai

first: Shenglin

address: 270 Dongan

country: China

institute: Fudan University

summary: Dedifferentiated liposarcoma (DDL) has the same cellular and molecular genetics features as well-differentiated liposarcoma (WDL), and there is still no ideal biomarker for the prediction of DDL patient prognosis in clinical practice. In order to explore the genes that cause WDL to obtain local invasion and distant metastasis capacities and transform it into DDL, The four DDL tissue specimens in this study were matched with four WDL tissue specimens according to baseline characteristics, such as gender, age, and recurrence, before high-throughput sequencing was conducted. Then total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

overall_design: Four tissue samples of dedifferentiated liposarcoma and corresponding matched well-differentiated liposarcoma were selected for high-throughput RNA sequencing

first: Lingge

last: Yang

first: Zhiqiang

last: Wu

first: Yong

first: Wangjun

last: Yan

first: Yan

last: Li

first: Chunmeng

last: Wang


title: Effects of sumoylation-impairing mutation of TFIIF subunit Tfg1 on genome-wide RNA polymerase II (RNAPII) levels in budding yeast

first: Emanuel

last: Rosonina

summary: Many transcription-related proteins, including components of the RNA polymerase II (RNAPII) general transcription factors (GTFs), have been shown through proteomics studies to be modifiable by SUMO conjugation. However, we determined that the large subunit of TFIIF, Tfg1, is likely the major target of sumoylation among GTFs in budding yeast. The primary site of sumoylation on Tfg1 is Lys residues 60 or 61, which lies in a region of the protein that is proximal to the Rpb2 subunit of RNAPII when the GTF-RNAPII preinitiation complex (PIC) assembles at promoters. As TFIIF and RNAPII are highly functionally and physically linked, we examined whether blocking Tfg1 sumoylation through Lys-to-Arg mutations could affect the recruitment or association of RNAPII with chromatin. RNAPII ChIP-seq was performed in strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. Indeed, nearly half of all protein-coding genes showed significantly reduced RNAPII levels in the mutant strain. These data suggest that sumoylation of TFIIF plays an important role in regulating the dynamics of RNAPII association with genes.

overall_design: Two independent replicates of RNAPII ChIP-seq from Tfg1-HA and Tfg1-K60,61R-HA strains.

first: Mohammad

last: Baig

first: Benjamin

last: Bergey


title: Comparative analysis of glioblastoma initiating cells and patient-matched EPSC-derived neural stem cells as a discovery tool and drug matching strategy [RNA-Seq]

first: Silvia

last: Marino

summary: Malignant gliomas are the most common intrinsic brain tumours in adults and are associated with a very poor prognosis, which has not improved in the last 20 years. We show here that glioblastoma initiating cells (GIC) and syngeneic neural stem cells derived from enhanced pluripotent stem cells (iNSC) are a suitable novel pre-clinical pipeline to discover new patient-specific disease mechanisms and to identify druggable targets for personalised therapy.

overall_design: Transcriptomic data of human dura mater fibroblasts, iPSC, iNSC, GIC and FFPE bulk tumour

last: Vinel

first: Gabriel

last: Rosser

first: Loredana

last: Guglielmi

first: Nicola

last: Pomella

first: Myrianni

last: Constantinou

first: Xinyu

last: Zhang

first: James

middle: R

last: Boot

first: Tania

last: Jones

first: Thomas

last: Millner

first: Anaelle

last: Dumas

first: Vardhman

last: Rakyan

first: Jeremy

last: Rees

first: Yau

last: Lim

first: Jamie

last: Thompson

first: Juho

last: Vuononvirta

first: Tedani

middle: E

last: Assan

first: Natasha

last: Aley

first: Yung-Yao

last: Lin

first: Pentao

last: Liu

first: Denise

last: Sheer

first: Catherine

last: Merry

first: Federica

first: Sebastian


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing  Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin[RNA-seq(QSC-Ctrl/sgMyc)]

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Skeletal muscle satellite cells (SCs) are muscle stem cells responsible for muscle development and injury induced muscle regeneration. The pace of SC related study, however, is constrained partially by the technological limitations in generating genetically modified mice. Although the ease of use of CRISPR-Cas9 in genome manipulation has been documented in many cell lines and various species, its application in endogenous SCs remains elusive. In this study, we generated muscle-specific Cas9-expressing mice and achieved robust in vivo genome editing in juvenile SCs at the postnatal stage through AAV9 mediated short guide RNAs (sgRNAs) delivery. We also found adult quiescent SCs are reluctant to CRISPR/Cas9 editing despite efficient AAV9 transduction. To edit juvenile SCs in vivo, as a proof-of-concept, we delivered sgRNAs targeting MyoD, a key gene critical for muscle physiology and showed an efficient editing at MyoD locus, resulting in accumulation of SCs and defects in SCs differentiation which resembled the phenotypes reported in MyoD knockout mice. Further application of this system on potential key transcription factors (TFs) involved in SC fate transition, Myc, Bcl6 and Pknox2, unveiled their distinct functions in the early stage of SC activation and injury induced muscle regeneration. In addition, we revealed that Myc orchestrated SCs activation through impinging on 3D chromatin architecture. Altogether we established a robust muscle restricted CRISPR/Cas9-based gene editing platform in endogenous SCs and elucidated the functionality of key factors governing SC activities.

overall_design: RNA-seq was performed in quiescent muscle stem cells isoalted from Pax7cas9 mice infected with AAV9-dual sgMyc virus.

first: Liangqiang

last: He

first: Yu

last: Zhao

first: Huating

last: Wang

first: Hao

last: Sun


title: Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

institute: FLI

summary:
Fibroblasts are activated to repair the heart following injury. Fibroblast
activation in the mammalian heart leads to a permanent fibrotic scar
that impairs cardiac function. In other organisms, such as zebrafish,
cardiac injury is followed by transient fibrosis and scar-free
regeneration. The mechanisms that drive scarring versus scar-free
regeneration are not well understood. Here, we show that the
homeobox-containing transcription factor Prrx1b is required for
scar-free regeneration of the zebrafish heart as the loss of Prrx1b
results in excessive fibrosis and impaired cardiomyocyte proliferation.
Through lineage tracing and single-cell RNA sequencing we find that
Prrx1b is activated in epicardial-derived cells where it restricts TGFβ
ligand expression and collagen production. Furthermore, through
combined in vitro experiments in human fetal epicardial-derived
cells and in vivo rescue experiments in zebrafish, we conclude that
Prrx1 stimulates Nrg1 expression and promotes cardiomyocyte
proliferation. Collectively, these results indicate that Prrx1 is a key
transcription factor that balances fibrosis and regeneration in the
injured zebrafish heart.

overall_design: Tg(tcf21:mCherry) positive cells (n=1438) were collected from cryoinjured hearts of wild-type (n = 20) and prrx1b-/- (n=20) ventricles. All cells were sent for single cell RNA sequencing.

first: Esther

last: Dronkers

first: Mara

last: Bouwman

first: Aryan

last: Vink

first: Marie

last: Goumans

first: Anke

last: Smits

first: Jeroen

last: Bakkers


title: Comparative analysis of glioblastoma initiating cells and patient-matched EPSC-derived neural stem cells as a discovery tool and drug matching strategy [Seq]

first: Silvia

last: Marino

overall_design: Transcriptomic and DNA methylation analysis of murine eNSC and two classes of induced NSC

first: Claire

last: Vinel

first: Nicola

last: Pomella


title: Viral Status Predicts Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma [Methylation]

status: Public on Sep 15 2021

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

country: USA

institute: University of Michigan

summary: To understand the global methylation patterns in MCC cell lines

overall_design: MCC cell lines' global methylation patterns are profiled by Infinium Methylation EPIC Array.

first: Paul

middle: W

last: Harm

first: Monique

last: Verhaegen

first: Josh

middle: N

last: Vo

first: Fengyun

last: Su

first: Jae

last: Choi

first: Andrzej

last: Dlugosz

first: Xuhong

last: Cao


title: Viral Status Predicts Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma


title: Viral Status Predicts Patterns of Genome Methylation and Decitabine Response in Merkel Cell Carcinoma [RNA-Seq]

summary: To understand the global methylation pattern in MCC

overall_design: MCC cell lines' global methylation patterns are profiled by Infinium Methylation EPIC Array. MCC cell lines are also treated with  5-aza-2’-deoxyazacitidine and/or trichostatin A and profiled for gene expression with RNA-seq.


title: A candidate RNAi screen reveals diverse RNA-binding protein phenotypes in Drosophila flight muscle

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

state: Bayern

address: Großhaderner Str. 9

department: Physiological Chemistry

institute: Ludwig-Maximilians-University München, Biomedical center

summary: The proper regulation of RNA processing is critical for muscle development and the fine-tuning of contractile ability among muscle fiber-types. RNA binding proteins (RBPs) regulate the diverse steps in RNA processing including alternative splicing, which generates fiber-type specific isoforms of structural proteins that confer contractile sarcomeres with distinct biomechanical properties. Alternative splicing is disrupted in muscle diseases such as myotonic dystrophy and dilated cardiomyopathy, and is altered after intense exercise as well as with aging. It is therefore important to understand splicing and RBP function, but currently only a small fraction of the hundreds of annotated RBPs expressed in muscle have been characterized. Here we demonstrate the utility of Drosophila as a genetic model system to investigate basic developmental mechanisms of RBP function in myogenesis. We find that RBPs exhibit dynamic temporal and fiber-type specific expression patterns in mRNA-Seq data and display muscle-specific phenotypes. We performed knockdown with 105 RNAi hairpins targeting 35 RBPs and report associated lethality, flight, myofiber and sarcomere defects, including flight muscle phenotypes for Doa, Rm62, mub, mbl, sbr, and clu. Interestingly, knockdown phenotypes of spliceosome components, as highlighted by phenotypes for A-complex components SF1 and Hrb87F (hnRNPA1), revealed level- and temporal-dependent myofibril defects. We further show that splicing mediated by SF1 and Hrb87F is necessary for Z-disc stability and proper myofibril development, and strong knockdown of either gene results in impaired localization of Kettin to the Z-disc. Our results expand the number of RBPs with a described phenotype in muscle and underscore the diversity in myofibril and transcriptomic phenotypes associated with splicing defects. Drosophila is thus a powerful model to gain disease-relevant insight into cellular and molecular phenotypes observed when expression levels of splicing factors, spliceosome components and splicing dynamics are altered.

overall_design: Analysis of differential gene expression and exon use in Drosophila IFM with knockdown of SF1 or Hrb87F. Design 1: SF1 RNAi IFM at 72h APF versus WT IFM at 72h APF ; Design 2: Hrb87F RNAi IFM at 72h APF versus WT IFM at 72h APF

first: Shao-Yen

last: Kao

first: Elena

last: Nikonova

first: Sabrina

last: Chaabane

first: Albiona

last: Sabani

first: Alexandra

last: Martitz

first: Anja

last: Wittner

first: Jakob

last: Heemken

first: Tobias

last: Straub

middle: L


title: Intrauterine growth restriction causes abnormal embyronic dentate gyrus neurogenesis in mouse offspring that leads to adult learning and memory deficits

city: Salt Lake City

first: Camille

last: Fung

state: UT

address: 295 Chipeta Way

department: Pediatric Neonatology

institute: University of Utah

summary: In our mouse model of intrauterine growth restriction (IUGR), we have discovered that IUGR promotes embyronic Sox2+ neural stem cell depletion as well as premature neurogenesis. Using RNA-seq, we strived to determine the differentially expressed molecular genes/pathways that may be responsible for such cellular differences between appropriately-grown and IUGR mouse offspring.

overall_design: Examination of sham and IUGR embryonic day 15.5 hippocampi

first: Tim

last: Mosbruger


title: CRISPR/Cas9/AAV9-sgRNA Mediated In Vivo Genome Editing Reveals the Indispensability of Myc During Muscle Stem Cells Activation by Remodeling the 3D Chromatin

city: Hong Kong

first: Yingzhe

last: Ding